instruction.txt

Calculate the normal modes, flexibility of residue and vibrationnal entropy of a structure.

For example with the structure 1ey0.pdb
./ENCoM/bin/build_encom -i 1ey0.pdb -cov 1ey0.cov -o 1ey0.eigen

This will create from the 1ey0 pdb files and cov file that represent the predicted flexibility of each residue and an eigen file that contains all the egeinvectors and eigenvalues. Note that the first 6 mode are non-trivial and should not be interpreted. 

use the flag -lig to consider HETAM in structure. A mass will be set a the center of mass of each unique residue.
Please note that this function is experimental and have not been validated

To generate conformations along one mode use the motion binarie file

For example, for motion of mode 10 and maximal distorsion of 2 of RMSD
./ENCoM/bin/motion -i 1ey0.pdb -m 10 -ieig 1ey0.eigen -p motion10.pdb -md 2.0